The invention pertains to a process for the microbial production of amino acids. The process involves boosting the export carrier activity and/or export gene expression of a microorganism which produces the desired amino acid. It was found that a single specific gene is responsible for the export of a given amino acid, and on that basis, a process for the microbial production of amino acids, involving the controlled boosting of the export gene expression and/or export carrier activity of a microorganism was developed, which produces the amino acid. The boosted expression or activity of the export carrier resulting from this process increases the secretion rate and thus increases transport of the desired amino acid.
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14. A process for the increased microbial production of amino acids using an export carrier gene, comprising the steps of:
i) constructing a gene construct including an export carrier gene,
ii) inserting said construct into a suitable vector,
iii) transforring a suitable host cell with said vector,
iv) cultivating said transformed host cell in a culture medium,
v) recovering the amino acid(s) from the culture, and
vi) determining the desired amino acid(s) amount.
1. A process for the microbacterial production of amino acids, comprising the steps of:
1) providing a microbial organism having amino acid export carrier activity and having export gene-expression,
2) increasing one of the export carrier activities of said microbial organism, wherein said export carrier has the amino acid sequence SEO ID NO: 2, and the export carrier activity is endogenous to said microbial organism, and
3) increasing the export gene expression of said export carrier, wherein said gene comprising nucleotides 1016 to 1726 of SEQ ID NO: 1 by means of one of the steps selected from the group of:
i) increasing the number of gene copies of the export carrier gene,
ii) modifying regulatory signals assigned to the export carrier gene, and
iii) amplifying regulatory signals assigned to the export carrier gene, whereby amino acids are produced by said microbial organism with increased efficiency, and
4) recovering the amino acids from the culture.
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This application is a continuation in part of PCT/DE96/02485 filed on Dec. 18, 1996, which claims benefit of a foreign (German) application 195 48 222.0 filed on Dec. 22, 1995.
The invention relates to a process for the microbial production of amino acids, to export genes, to regulator genes, to vectors, to transformed cells, to membrane proteins, and to uses.
Amino acids are of high economical interest and there are many applications for the amino acids: for example, L-lysine as well as L-threonine and L-tryptophan are needed as feed additives, L-glutamate as seasoning additive, L-isoleucine, and L-tryosine in the pharmaceutical industry, L-arginine and L-isoleucine as medicine or L-glutamate and L-phenylalanine as a starting substance for the synthesis of fine chemicals.
A preferred method for the manufacture of these different amino acids is the biotechnological manufacture by means of micro-organisms; since, in this way, the biologically effective and optically active form of the respective amino acid is directly obtained and simple and inexpensive raw materials can be used. As microorganisms, for example, Corynebacterium glutamicum and its relatives ssp. flavum and ssp lactofermentum (Liebl et al; Int. J-System Bacteriol (1991) 41:255-260) as well as Escherichia coli and related bacteria can be used.
However, these bacteria produce the amino acids only in the amounts needed for their growth such that no excess amino acids are generated and are available. The reason for this is that in the cell the biosynthesis of the amino acids is controlled in various ways. As a result, different methods of increasing the formation of products by overcoming the control mechanisms are already known. In these processes, for example, amino acid analogs are utilized to render the control of the biosynthesis ineffective. A method is described, for example, wherein Corynebacterium strains are used which are resistant to L-tyrosine and L-phenylalanine analogs (JP 19037/1976 and 39517/1978). Also methods have been described in which bacteria resistant to L-lysine and also to L-threonine analogs are used in order to overcome the control mechanisms (EP 0 205 849 B1, UK patent application GB 2 152 509 A).
Furthermore, microorganisms constructed by recombinant DNA techniques are known wherein the control of the biosynthesis has also been eliminated by cloning and expressing the genes which code for the key enzymes which cannot be feed-back inhibited any more. For example, a recombinant L-lysinee producing bacterium with plasmid-coded feedback-resistant aspartate kinase is known (EP 0381527). Also, a recombinant L-phenylalanine producing bacterium with feedback resistant prephenate dehyrodgenase has been described (JP 124375/1986; EP 0 488 424). In addition, increased amino acid yields have been obtained by overexpression of genes which do not code for feedback-sensitive enzymes of the amino acids synthesis. For example, the lysine formation is improved by increased synthesis of the dihydrodipicolinate synthase (EP 0 197 335). Also, the threonine formation is improved by increased synthesis of threonine dehydratase (EP 0 436 886 Al).
Further experiments for increasing the amino acid production aim at an improved generation of the cellular primary metabolites of the central metabolism. In this connection, it is known that the overexpression of the transketolase achieved by recombinant techniques improve the product generation of L-tryptophan, L-tyrosine or L-phenalanine (EP 0 600 463 A2). Furthermore, the reduction of the phosphenol pyruvate carboxylase activity in Corynebacterium provides for an improvement in the generation of aromatic amino acids (EP 0 331 145).
All these attempts to increase the productivity have the aim to overcome the limitation of the cytosolic synthesis of the amino acids. However, as a further limitation basically also the export of the amino acids formed in the interior of a cell into the culture medium should be taken into consideration. As a result, it has been tried to improve this export and, consequently, the efficiency of the amino acid production. For example, the cell permeability of the Corynebacterium has been increased by biotin deficiency, detergence or penicillin treatment. However, these treatments were effective exclusively in the production of glutamate, whereas the synthesis of other amino acids could not be improved in this manner. Also, bacteria strains have been developed in which the activity of the secretion system is increased by chemical or physical mutations. In this way, for example, a Corynebacterium glutamicum strain has been obtained which has an improved secretion activity and is therefore especially suitable for the L-Lysine production. (DE 02 03 320).
Altogether, the attempts to increase the secretion of amino-acids formed within the cell have all in common that an increase efflux of amino acids on the basis of the selected non-directed and non-specific methods could be achieved only accidentally.
Solely in the German patent application No. 195 23 279.8-41, a process is described which provides for a well-defined increase of the secretion of amino acids formed internally in a cell by increasing the expression of genes coding for the import of amino acids. The understanding on which this process was based, that is, the cell utilizes import proteins for the export of amino acids as well as the fact that by nature microorganisms do not generate and release excess amino acids lets one assume that export genes or proteins specific for the amino acid transport do not exist, but that the amino acids are excreted by way of other export systems.
The export systems known so far export poisonous metal ions, toxic antibiotica and higher molecular toxins. These export systems are relatively complex in their structure. Generally, membrane proteins of the cytoplasmic membrane are involved which however cause only a partial reaction of the export so that presumably additional extra cytoplasmic support proteins are needed for the transport (Dink, T. et al., A family of large molecules across the outer membranes of gram-negative bacteria., J. Bacteriol. 1994, 176: 3825-3831). Furthermore, it is known that, with the sec-dependent export system for extra-cellular proteins, at least six different protein components are essential for the export. This state-of-the-art suggests that also the systems, which are responsible for the export of amino acids, but which are not known so far comprise several protein components or respectively, several genes are responsible for the export of amino acids. A hint in this direction could be the various mutants which are defective in the lysine export as described by Vrylic et al.,(J. Bacteriol (1995) 177:4021-4027).
It has now been found surprisingly that only a single specific gene is responsible for the export of amino acids so that, in accordance with the invention, for the first time a method for the microbial manufacture of amino acids is provided wherein clearly the export gene expression and/or the export carrier activity of a microorganism producing amino acids is increased. The increased export expression or respectively, activity of the export carrier resulting from this process leads to an increased secretion rate so that the export of the respective amino acid is increased. The microorganisms so modified also accumulate an increased part of the respective amino acid in the culture medium.
For an increase in the export carrier activity especially the endogenic activity of an amino acid producing microorganism is increased. An increase of the enzyme activity can be obtained for example by an increased substrate consumption achieved by changing the catalytic center or by eliminating the effects of enzyme inhibitors. An increased enzyme activity can also be caused by an increased enzyme synthesis for example by gene amplification or by eliminating factors which inhibit the enzyme biosynthesis. The endogene export activity is increased preferably by mutation of the endogenic export gene. Such mutations can be generated either in an uncontrolled manner in accordance with classic methods as for example by UV irradiation or by mutation causing chemicals or in a controlled manner by gene-technological methods such as deletion(s) insertion(s) and/or nucleotide exchange(s).
The export gene expression is increased by increasing the number of gene copies and/or by increasing regulatory factors which positively affect the export gene expression. For example, a strengthening of regulatory elements takes place preferably on the transcription level by increasing particularly the transcription signals. This can be accomplished for example in that, by changing the promoter sequence arranged before the structure gene, the effectiveness of the promoter is increased or by completely replacing the promoter by more effective promoters. An amplification of the transcription can also be achieved by accordingly influencing a regulator gene assigned to the export gene as will be explained further below. On the other hand, an amplification of the translation is also possible, for example, by improving the stability of the m-RNA.
To increase the number of gene copies the export gene is installed in a gene construct or, respectively, in a vector, preferably, a vector with a small number of copies. The gene construct includes regulatory gene sequences, which are specifically assigned to the export gene, preferably such sequences, which re-inforce the gene expression. The regulatory gene sequences comprise a nucleotide sequence which codes for the amino acid sequence SEQ ID No.(B)3 and given in table 1 or the allele variations thereof or respectively, a nucleotide sequence 1421 to 2293 according to SEQ ID No. (B)1shown in table 2 or a DNA sequence which is effective essentially in the same manner.
Allele variations or, respectively, equally effective DNA sequences comprise particularly functional derivatives which can be obtained by deletion(s) insertion(s) and/or substitution(s of nucleotides of corresponding sequences, wherein however the regulator protein activity or function is retained or even increased. In this way, the effectiveness of the interaction of the regulatory protein to the DNA of the export gene to be regulated can be influenced by mutating the regulatory gene sequence such that the transcription is strengthened and, consequently, the gene expression is increased. In addition, also so-called enhancers may be assigned to the export gene as regulatory sequences whereby, via an improved correlation between RNA polymerase and DNA, also the export gene expression is increased.
For the insertion of the export gene into a gene construct, the gene is preferably isolated from a microorganism strain of the type Corynebacterium and, with the gene construct including the export gene, a microorganism strain, especially Corynebacterium, producing the respective amino acid is transformed. The isolation and transformation of the respective transport gene occurs according to the usual methods. If a transport gene is isolated and cloned from Corynebacterium then for example, the method of homologuous complementation of an export defective mutant is suitable (J.Bacteriol. (1995)177: 4021-4027). If a direct cloning of the structure gene is not possible vector sequences may first be inserted into the transport gene whereupon it is isolated by way of “plasmid rescue” in the form of inactive fragments. For the process according to the invention genes from the C. glutamicum ATCC 13032 or C. glutamicum ssp. flavum 14067 or also, C. glutamicum ssp. lacto fermentum ATCC 13869 are particularly suitable. The isolation of the genes and their invitro recombination with known vectors (Appl. Env. Microbial (1989)55: 684-688; Gene 102(1991)93-98) is followed by the transformation into the amino acid producing strains by electroporation (Liebl et al. (1989)FEMS Microbiol Lett. 65; 299-304) or conjugation (Schafer et al. (1990) J. Bacteriol. 172:1663-1666). For the transfer, preferably vectors with low numbers of copies are used. As host cells, preferably such amino acid producers are used which are deregulated in the synthesis of the respective amino acids and/or which have an increased availability of central metabolism metabolites.
After isolation, export genes with nucleotide sequences can be obtained which code for the amino acid sequences given in SEQ ID No.(A)2 and shown in table 3 or for their allele variations or, respectively, which include the nucleotide sequence of 1016 to 1726 according to SEQ ID No. (A) 1 and table 2 or a DNAy sequence which is effective essentially in the same way. Also here, allele variations or equally effective DNA sequences include particularly functional derivatives in the sense indicated above for the regulatory sequences. These export genes are preferably used in the process according to the invention.
One or several DNA sequences can be connected to the export gene with or without attached promoter or respectively, with or without associated regulator gene, so that the gene is included in a gene structure.
By cloning of export genes, plasmids or, respectively, vectors can be obtained which contain the export gene and which, as already mentioned, are suitable for the transformation of an amino acid producer. The cells obtained by transformation which are mainly transformed cells from Corynebacterium, contain the gene in reproducible form, that is, with additional copies on the chromosome wherein the gene copies are integrated at any point of the genome by homologous recombination and/or on a plasmid or respectively, vector.
A multitude of sequences is known which code for membrane proteins of unknown function. By providing in accordance with the invention export genes such as the export gene with the nucleotide sequence of nucleotide 1016 to 1726 in accordance with SEQ ID No. 1 and table 2 or respectively, the corresponding export proteins for example that with the amino acid sequence according to SEQ ID No. 2, it is now possible to identify by sequence comparison membrane proteins, whose function is the transport of amino acids. The export gene identified in this way can subsequently be used to improve the amino acid production in accordance with the process of the invention.
The membrane proteins known from the state-of-the-art generally include 12, some also only 4 transmembrane helices. However, it has now been found surprisingly that the membrane proteins responsible or suitable for the export of amino acids include 6 transmembrane helices (see for example, the amino acid sequence of an export protein listed in SEQ ID No. 2 and table 3, wherein the 6 transmembrane areas have been highlighted by underlining). Consequently, there is a new class of membrane proteins present, which has not yet been described.
a) Cloning of an export gene and cloning of a regulator of Corynebacterium glutamicum.
Chromosomal DNA from C. glutamicum R127 (FEMS Microbiol lett. (1989)65:299-304) was isolated as described by Scharzer et al. (Bio/Technology (1990) 9:84-87). The DNA was then split with the restriction enzyme Sau3A and separated by saccharose gradient centrifugation as described in Sambrook et al. (Molecular cloning, A laboratory manual (1989) Cold Spring Harbour Laboratory Press). The various fractions were analyzed gel electrophoretically with respect to their size and the fraction with a fragment size of about 6-10 kb was used for the ligation with the vector pJCl. In addition, the vector pJCl was linearized with BamHI and dephosphorylized. Five ng thereof was ligated with 20 ng of the chromosomal 6-10 kb fragments. With the whole ligation preparation, the export defective mutant NA8 (J. Bacterol. (1995)177:4021-4027) was transformed by electroporation (FEMS Microbiol Lett(1989)65:299-304). The transformants were selected for LBHIS(PEMS Microbiol. Lett. (1989)65:299-304) with 15 μg kanamycin per ml. These transformants were subjected to extensive plasmid analyses in that 200 of the altogether 4500 clones obtained were individually cultivated and their plasmid content and size was determined. On average, about half of the kanamycin-resistant clones carried a recombinant plasmid with an insert of the average size of 8 kb. This provides for a probability of 0.96 for the presence of any gene of C. glutamicum in the established gene bank. The 4500 obtained transformants were all individually checked for renewed presence of lysinee secretion. For this purpose, the system described by Vrljic for the induction of the Llysinee excretion in Corynebacterium glutamicum was utilized (J. Bacteriol (1995) 177:4021-4027). For this purpose, so-called minimal-medium-indicator plates were prepared, which contained per liter 20 g (NH4)2SO4, 5 g uric acid, 1 g KH2PO4, 1 g K2HPO4, 0.25 g MgSO4×7H2O, 42 g morpholino propane sulfonic acid, 1 ml CaCl2 (1 g/100 ml), 750 ml dest., 1 ml Cg trace salts, 1 ml biotin (20 μg/1001), pH7, 4% glucose, 1.8 mg protocatechuic acid, 1 mg FeSO4×7 H2O, 1 mg MnSO4×H2O, 0.1 mg ZnSO4×7 H2O, 0.02 mg CuSO4, 0.002 mg NiCl2×6 H2O, 20 g agar-agar, as well as 107 cells/ml of the lysine-auxotrophene C. glutamicum mutant 49/3. The original 4500 transformants were all individually pinned, by toothpicks onto the indicator plates with, in each case, a check of the original non-excretor NAB (J.Bacteriol (1995)177:4021-4027) and the original strain R127. At the same time, always 2 plates were inoculated of which only one contained additionally SmM L-methionine in order to induce the lysine excretion in this way.
The indicator plates were incubated at 30° C. and examined after 15, 24 and 48 hours. In this way, altogether 29 clones were obtained which showed on the indicator plate provided with methionine a growth court by the indicator strain 49/3. The clones were examined individually and then again as described above, for reestablishment of the growth court. In this way, the two clones NA8 pMVB-5-24 and NA8 pMV6-3 were obtained which had again received the capability to excrete lysine.
From these clones, plasmid preparations were performed as described in Schwarzer et al. (Bio/Technology (1990)9; 84-87). By retransformation in NA8, the plasmid-connected effect of the excretion of L-lysine was confirmed. Both plasmids were subjected to a restriction analysis. Plasmid pMVB-5-24 carries an insert of 8.3 kb, and pMV6-3 one of 9.5 kb. The physical charter of the inserts is shown in FIG. 1.
b) Subcloning of an DNA fragment which reconstitutes the lysine export.
From the insert of the plasmid pMV6-3 individual subclones were prepared utilizing the restriction severing point as determined. In this way, the 3.7 kb XhoI-SalI-fragment, the 2.3 kb BamHI-fragment and the 7.2 kb BamHI fragment were ligated with the correspondingly severed and treated vector pJCl (Mol Gen. Genet.(1990)220: 478-480). With the ligation products C. glutamicum NA8 was directly transformed, the transformants were tested for having the lysine excretion properties and the presence of the subclone was confirmed by plasmid preparation and restriction analysis. In this way, the strain with plasmid pMV2-3 (
c) Sequence of the lysine export gene lys E and its regulators lysG.
The nucleotide sequence of the 2.3 kb BamH1 fragment was performed according to the dideoxy-chain termination method of Sanger et al. (Proc. Natl. Acad. Sci USA(1977) 74:5463-5467) and the sequencing reaction with the Auto Read Sequencing kit from Pharamcia (Uppsala, Sweden). The electrophoretic analysis occurs with the automatic laser-fluorescence DNA sequencing apparatus (A.L.F) from Pharmacia-LKB(Piscataway, N.J., USA). The nucleotide sequence obtained was analyzed by the program packet HUSAR (Release 3.0) of the German Cancer Research Center (Heidelberg). The nucleotide sequence and the result of the analysis is presented in SEQ ID No 1 and FIG. 2. The analysis results in two fully open reading frames (ORF) on the sequenced DNA piece. ORF1 codes for a protein with a length of 236 amino acids, OFR2 codes for a protein with a length of 290 amino acids. The protein derived from ORF1 includes an accumulation of hydrophobic amino acids as they are characteristic for membrane-embedded proteins. The detailed analysis of the distribution of the hydrophobic and hydrophilic amino acids by the programs PHD.HTM (Protein Science(1995)4:521-533) is shown in table 3. It is apparent therefrom that the protein contains six hydrophobic helix areas which extend through the membrane. Consequently, this protein is the searched for exporter of the amino acid L-lysine. The corresponding gene will therefore be designated below as lysE. In table 2, it is marked accordingly. ORF2 is transcribed in a direction opposite to ORF1. The sequence analysis shows that ORF2 has a high identity with regulator genes which are combined as a single family (Ann Rev Microbiol(1993) 597-626). Genes of this family regulate the expression processes of the various genes involved in catabolic or anabolic processes in a positive way. For this reason, ORF2 will below be designated as lysG (Govern=regulating). Because of the coordination and because IysE could be cloned (see a)) and subcloned (see b)) together with lysG, lysG is regulator of lysE and consequently also participates in the lysine export. The gene lysG and the amino acid sequence derived therefrom are also shown in SEQ ID No(B)1 and table 2 and, respectively, SEQ ID No.3.
d) Identification of an unknown membrane protein from Escherichia coli by sequence comparison.
With the established sequences according to table 3 already existing sequence banks can be searched in order to assign the proteins derived in this way from sequenced areas a certain function. Correspondingly, the amino acid sequence of the lysine exporters consisting of C. glutamicum were compared with derivated protein sequences of all the DNA sequences deposited there utilizing the program packet HUSAR (Release 3.0) of the German Cancer Research Center (Heidelberg). A high homology of 39.3% identical amino acids and 64.9% similar amino acids was found to a single sequence of so far unknown function of E. coli.
The comparison is shown in FIG. 2. The open read frame of E. coli so far not characterized is consequently identified by way of this process as an amino export gene.
e) Increased export of intracellularly accumulated L-lysine.
The strain C. glutamicum NA8 (J. Bacteriol(1995) 177: 4021-4027 was transformed with plasmid pMV2-3 and the L-lysine excretion of the strains was compared. For this purpose, NA8 and NA8pMV2-3 in complex medium were utilized as described in Vrljic et al. (J. Bacteriol (1995)177:4021-40277) and the fermentation medium CGXII (Bacteriol (1993)175:5595-5603 were each separately inoculated. The medium additionally contained 5rnM L-methionin in order to induce the intracellular L-lysine biosynthesis. After cultivation for 24 hours at 30° C. on a rotary vibrator at 140 rpm, the cell internal and external L-lysine determinations were performed. For the cell-internal determination silicon oil centri-fugations were performed (Methods Enzymology LV(1979) 547-567); the determination of the amino acids occurred by high pressure liquid chromatography (J. Chromat (1983) 266:471-482). These de. terminations were performed at different times as indicated in FIG. 3. In accordance with the process used the retained cell internal L-lysine is excreted also by pMV2-3 to a greater degree and is accumulated. Accordingly, also the cell internally present L-lysine is greatly reduced. Consequently, the utilization of the newly discovered and described exporter represents a process for greatly improving the L-lysine production.
f) Increased accumulation of L-lysine by lysE or LysEG.
From the subclone pMV2-3 which contains the sequenced 2374 bp Bam HI-fragment in pJCI (see FIG. 1), the lysE carrying 1173 bpPvuII fragment was ligated in pZ1 (Appl. Env. Microbiol (1989)55:684-688) according to the sequence information and in this way, the plasmid plysE was obtained. This plasmid as well as the lysE lysG carrying plasmid pMV2-3 was introduced into C. glutamicum strained by electroporation wherein the chromosomal areas were deleted. The obtained strains C. glutamicum d pMV2-3, C. glutamicum d plysE, C. glutamicum pJCl were, as described under e) precultivated on a complex medium, then cultivated in production minimal medium CGx11 together with 4% glucose and 5 mM 1-methionin and samples were taken to determine the accumulated lysine. As apparent from
Table 1: The amino acid sequence of the lysine exporter regulator from Corynebacterium glutamicum with the helix-turn-helix motive typical for DNA-binding proteins.
Table 2(three pages): The nucleotide sequence of C. glutamicum coding for the lysine exporter and lysine export regulators.
Table 3: the amino acid sequence of the lysine exporter from Corynebacterium glutamicum with the identified transmembrane helices TMH1 to TMH6.
Sequence Protocol A:
Sahm, Hermann, Eggeling, Lothar, Vrlijc, Marina
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